Table 1.
Selected ontologies of commonly upregulated genes
| Term | Genes a | Gene set on the array | Z-score |
|---|---|---|---|
| Biological process | |||
| Response to stimulus | 39 | 3,137 | 4.82 |
| Response to stress | 27 | 1,753 | 5.05 |
| Response to unfolded proteinb | 3 | 62 | 4.14 |
| Acute inflammatory responseb | 5 | 99 | 5.5 |
| Acute-phase responseb | 4 | 43 | 7.11 |
| Regulation of acute inflammatory responseb | 3 | 26 | 6.95 |
| Response to chemical stimulus | 21 | 1,396 | 4.26 |
| Response to organic substanceb | 15 | 845 | 4.25 |
| Response to hormone stimulusb | 10 | 440 | 4.35 |
| Response to steroid hormone stimulusb | 7 | 220 | 4.75 |
| Response to glucocorticoid stimulusb | 6 | 94 | 6.98 |
| Leukocyte chemotaxisb | 3 | 60 | 4.23 |
| Response to oxygen levelsb | 5 | 151 | 4.12 |
| Response to toxinb | 3 | 64 | 4.05 |
| Response to extracellular stimulus | 7 | 242 | 4.41 |
| Positive regulation of response to external stimulusb | 4 | 87 | 4.63 |
| Cellular response to extracellular stimulusb | 5 | 82 | 6.19 |
| Cellular response to nutrient levelsb | 4 | 62 | 5.73 |
| Cellular response to starvationb | 3 | 43 | 5.2 |
| Response to biotic stimulus | 10 | 424 | 4.49 |
| Response to virusb | 6 | 147 | 5.24 |
| Cell death | 24 | 1,227 | 6.04 |
| Apoptosis | 22 | 1,116 | 5.8 |
| Regulation of cell deathb | 17 | 872 | 4.99 |
| Regulation of apoptosisb | 16 | 859 | 4.62 |
| Negative regulation of cell deathb | 10 | 402 | 4.69 |
| Negative regulation of apoptosisb | 9 | 391 | 4.16 |
| Induction of apoptosisb | 8 | 333 | 4.06 |
| Anti-apoptosisb | 8 | 226 | 5.49 |
| Positive regulation of anti-apoptosisb | 3 | 32 | 6.18 |
| Cellular component disassembly involved in apoptosisb | 3 | 27 | 6.81 |
| Release of cytochrome c from mitochondriab | 3 | 24 | 7.27 |
| Protein folding | 6 | 158 | 4.99 |
| Leukocyte migration | 4 | 86 | 4.66 |
| Autophagy | 3 | 48 | 4.86 |
| Regulation of synaptic plasticity | 3 | 57 | 4.37 |
| Iron ion homeostasis | 4 | 31 | 8.54 |
| Positive regulation of smooth muscle cell proliferation | 3 | 28 | 6.67 |
| Regulation of viral reproduction | 3 | 28 | 6.67 |
| Cellular component | |||
| Integral to membrane | 9 | 4,459 | -4.27 |
| Autophagic vacuole | 3 | 20 | 8.2 |
| Molecular functions | |||
| Heat-shock protein binding | 5 | 71 | 7.14 |
| Unfolded protein binding | 5 | 103 | 5.69 |
| Antioxidant activity | 3 | 45 | 5.35 |
aNumber of genes differentially expressed within the assigned ontology. bSubcategory within a given ontology.